I have seen this Bethesda bug reported elsewhere, but it is particularly troublesome with this mod if you are not aware of it.

What happens is if you access a Companion's Inventory via the Trade option, and equip/Unequip an item they are wearing, the Game engine temporarily removes all Spell Effects from that NPC then re-applies them. Noone knows why (theory is to recalculate base resistances/buffs). The problem is it doesn't re-apply all the effects, which is a problem for constant effects.

Effects that are lost seem to be:
- ones applied via scripts (actor.cast(spell))
- ones attached to Actor aliases on quests - a common method used by mods (e.g. Better Companions, and this Mod's 'no conflicts' version)
- ones that run a script extending the magiceffect - the script ends but is never restarted (as used by this mod)

There could be more, but this is what is reported, and verified by me.

The effects/buffs are only restored if you exit the game and restart from that Exitsave. Fast travel does not fix it.
It seems re-entering PowerArmor also fixes it - a solution for this mod (get the Companion to exit and re-enter PA), though restart is easier...

This is not just a problem for Mods either. If your companion is in PowerArmor, and you use Trade to equip/unequip a clothing item (say a hat), all their PowerArmor perks are lost (No fall damage, immude to fire, jump boost, Rad resistance etc).

The takeaway from this is avoid changing what you Companions wear, or if you do then restart your game afterwards.
Obviously if you have no mods effected by this, and they are not in PA, then you have no issues.
This bug nukes my Mod for the companions, however.

Note: The player is not effected by this bug.